[BioC] biomaRt column order

[Mark Robinson]

Dear list.

I'm using biomaRt to do a fairly simple query against the Ensembl  
human database.  I get returned a table with column names that don't  
match the data in the columns.  See below.

I can reshuffle them afterwards to make them, but thats not ideal.

Am I doing something wrong?

Thanks,
Mark




 > library(biomaRt)
Loading required package: RCurl
 > mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
Checking attributes and filters ... ok
 > mart
Object of class 'Mart':
  Using the ensembl BioMart database
  Using the hsapiens_gene_ensembl dataset
 > b<- 
getBM 
(c 
("ensembl_gene_id 
","chromosome_name 
","sequence_biotype 
","sequence_exon_chrom_start 
","sequence_exon_chrom_end 
"),filters="ensembl_gene_id",values="ENSG00000197530",mart=mart)
 > dim(b)
[1] 25  5
 > b[1:10,]
    ensembl_gene_id chromosome_name struct_biotype exon_chrom_start
1   protein_coding         1542803        1542958  ENSG00000197530
2   protein_coding         1548674        1548942  ENSG00000197530
3   protein_coding         1549017        1549188  ENSG00000197530
4   protein_coding         1550038        1550144  ENSG00000197530
5   protein_coding         1550234        1550428  ENSG00000197530
6   protein_coding         1550529        1550671  ENSG00000197530
7   protein_coding         1551893        1551997  ENSG00000197530
8   protein_coding         1552080        1552242  ENSG00000197530
9   protein_coding         1552317        1552450  ENSG00000197530
10  protein_coding         1552539        1552687  ENSG00000197530
    exon_chrom_end
1               1
2               1
3               1
4               1
5               1
6               1
7               1
8               1
9               1
10              1
 > sessionInfo()
R version 2.7.1 (2008-06-23)
i386-apple-darwin8.10.1

locale:
en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_1.14.0 RCurl_0.9-3

loaded via a namespace (and not attached):
[1] XML_1.95-2



------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852